Soil pores are dominated in various soil functions, including water infiltration and retention, soil permeability, nutrient availability, as well as aeration and mechanical impedance to root elongation. The dynamic behavior of soil pores is primarily influenced by tillage practices, the presence of crop roots, and the return of soil organic matter. In this research, a systematic investigation was implemented to explore the impacts of the long-term application of organic fertilizers and straw on the soil pore structure. An analysis was also made to elucidate the relationship between soil organic carbon and soil pore structure. The data was collected from a 16-year long-term field experiment located in Shui Tou agricultural experimental base, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Yuncheng, Shanxi Province. Four treatments were set as sole chemical fertilizer (F), organic fertilizer + chemical fertilizer (MF), straw returning + chemical fertilizer (SF), and organic fertilizer + straw returning + chemical fertilizer (MSF). The soil pore structure was examined using X-ray computed tomography (CT) and advanced image processing. While the soil organic carbon was assessed to determine the physical fraction contents (free particulate organic matter (FPOM), occluded particulate organic matter (OPOM), and mineral-associated organic matter (MOM)). Additionally, the structural properties of the organic carbon were qualitatively and quantitatively analyzed by Fourier transform infrared (FTIR) spectroscopy. The results indicated that all organic amendment treatments significantly enhanced the total porosity and porosity of >0.5 mm aperture, compared with the F treatment (P<0.05). Notably, the MSF treatment exhibited the highest values. Specifically, the total porosity and porosity of >0.5 mm aperture increased by 61.6% 66.2%, 23.0% and 31.1%, and 16.8% and 13.5%, respectively, compared with the F, MF, and SF treatments. Additionally, the porosity ranging from 0.5 to 0.2 mm in the MF and MSF treatments was significantly higher than that in the F treatment (P<0.05). However, there was no significant difference in porosity ranging from 0.2 to 0.06 mm among all treatments. Furthermore, MSF treatment significantly enhanced the connectivity and complexity of soil pores, with increases of 33.2% and 17.9%, respectively, compared with the F treatment P<0.05). The organic fertilizer and straw returning treatments (SF, MF, and MSF) achieved a significant increase (P<0.05) in the contents of total soil organic carbon, FPOM, OPOM, and MOM. MSF also exhibited the highest values among these treatments, with concentrations of 21.5, 7.1, 4.2, and 10.2 g/kg, respectively. The long-term straw incorporation and the application of organic fertilizers (MSF) were performed better to accumulate the polysaccharide and lipid organic carbon in the soil, while concurrently reducing the content of aromatic organic carbon. The Pearson correlation analysis revealed that there was a positive and significant relationship between soil total porosity, porosity of >0.5 mm aperture, as well as the connectivity and complexity of soil pores with the contents of total soil organic carbon, FPOM, OPOM, MOM, and polysaccharide and lipid organic carbon (P<0.05). These findings suggested that the application of organic fertilizer and straw incorporation enhanced the content of soil organic carbon to accumulate the polysaccharide and lipid organic carbon, which facilitated the formation and modification of soil pores. Consequently, the enhanced physical properties of the soil were attributed to the regulation of soil structure by the organic amendment. An optimal distribution of soil pores was achieved to increase the soil complexity and pore connectivity. Accordingly, the organic amendment can be an effective strategy to optimize the soil pore structure. Future studies should also examine the response of soil pore structure and pore size distribution to the decomposition of incorporated organic manure